Contacts of the strand formed by residues 299 - 308 (chain B) in PDB entry 2IFG
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with TRP 299 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B ALA* 4.0 25.1 - - + -
294B VAL 3.5 15.9 - - - -
295B GLU* 3.2 53.5 + - + +
298B HIS* 1.3 78.6 - - - +
300B CYS* 1.3 62.6 + - - +
347B ARG* 3.5 4.3 - - - -
348B LEU* 3.0 48.9 + - + +
350B GLN* 5.4 1.1 - - - -
351B PRO* 3.6 26.9 + - + +
377B ALA 3.7 16.8 - - - -
378B PHE* 3.5 43.7 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B ALA* 3.3 2.2 - - - -
294B VAL* 2.7 44.0 + - - +
296B MET* 4.2 17.0 - - + -
298B HIS* 4.7 2.2 - - + +
299B TRP* 1.3 80.0 - - - +
301B ILE* 1.3 64.3 + - - +
302B PRO* 3.2 27.6 - - - +
345B CYS* 2.0 48.5 - - + -
346B LEU 3.3 5.6 - - - -
347B ARG* 5.1 2.2 - - + -
348B LEU* 4.5 0.7 - - - -
6F ILE* 4.4 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B LEU* 4.2 4.0 - - + -
291B HIS 3.9 9.0 - - - +
293B ALA* 4.1 15.0 - - + +
300B CYS* 1.3 77.1 - - - +
302B PRO* 1.3 66.7 - - - +
303B PHE* 3.7 2.3 + - - -
315B TRP* 3.9 14.6 - - + -
345B CYS* 3.2 1.2 - - - -
346B LEU* 3.0 48.7 + - + +
348B LEU* 4.2 12.6 - - + -
359B TYR* 3.6 40.2 - - + -
374B ILE* 3.8 24.9 - - + -
376B ALA* 4.4 9.2 - - + -
378B PHE* 4.8 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 302 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B LEU* 3.4 5.5 - - - +
291B HIS* 2.9 46.2 + - + +
292B THR 3.6 17.0 - - - +
294B VAL* 3.8 12.8 - - + -
300B CYS* 3.2 26.9 - - - +
301B ILE* 1.3 85.6 - - - +
303B PHE* 1.3 58.2 + - - +
344B GLY 3.3 10.8 - - - +
4F HIS* 4.0 21.5 - - + +
6F ILE* 4.1 8.7 - - + -
7F PHE* 4.9 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 303 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B GLN 3.3 9.2 - - - +
290B LEU* 4.1 4.9 - - + -
291B HIS* 4.7 0.9 - - - -
301B ILE 4.3 1.3 - - - +
302B PRO* 1.3 74.6 - - - +
304B SER* 1.3 66.5 + - - +
305B VAL* 3.8 12.8 - - + -
313B LEU* 3.8 16.4 - - + -
315B TRP* 4.3 11.2 - + + -
330B THR* 3.9 12.6 - - + -
331B GLU 4.0 0.4 - - - -
332B PHE* 3.3 42.0 - + - -
342B ARG 4.5 0.4 - - - -
343B HIS* 3.3 2.5 - - - -
344B GLY* 3.0 49.7 + - - -
345B CYS* 3.2 35.9 - - - -
361B LEU* 3.5 29.2 - - + -
4F HIS* 3.2 8.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 304 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B VAL* 3.5 3.3 - - - +
289B GLN* 3.0 54.4 + - - +
291B HIS* 4.1 4.2 + - - -
303B PHE* 1.3 75.2 - - - +
305B VAL* 1.3 60.6 + - - +
341B VAL* 4.7 4.3 - - - -
342B ARG 3.3 5.4 - - - -
343B HIS* 2.8 31.3 + - - -
4F HIS* 3.4 14.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B SER 3.3 14.1 - - - +
288B VAL* 3.5 20.2 - - + -
303B PHE* 3.8 24.9 - - + -
304B SER* 1.3 75.2 - - - +
306B ASP* 1.3 63.5 + - - +
311B PRO* 3.5 29.3 - - + +
313B LEU* 4.1 15.3 - - + -
332B PHE* 4.6 1.6 - - + -
340B THR 4.3 1.0 - - - +
341B VAL* 3.6 3.3 - - - +
342B ARG* 2.9 52.3 + - + +
361B LEU* 5.3 0.7 - - + -
363B ALA* 3.6 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B PHE* 3.1 25.5 - - + -
286B ALA* 3.3 6.9 - - - +
287B SER* 3.1 42.6 + - - +
305B VAL* 1.3 79.2 - - - +
307B GLY* 1.3 76.5 + - - +
311B PRO* 3.8 6.5 - - - +
340B THR* 3.2 19.6 + - - -
341B VAL* 3.8 24.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 307 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B PHE* 3.5 13.8 - - - -
285B PRO 3.6 11.2 - - - -
286B ALA* 4.0 4.7 - - - -
306B ASP* 1.3 91.9 + - - +
308B GLN* 1.3 64.6 + - - +
309B PRO 3.1 14.8 - - - +
310B ALA* 3.3 14.3 - - - +
311B PRO* 4.0 2.0 - - - +
340B THR* 4.7 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 308 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B ASN* 3.9 11.0 - - - +
260B ARG* 4.5 5.4 - - - +
281B ASN* 4.3 18.8 + - - +
282B VAL 3.2 20.3 - - - +
283B SER* 2.6 13.0 - - - -
284B PHE* 2.2 70.3 + - + +
307B GLY* 1.3 73.2 + - - +
309B PRO* 1.3 85.2 + - - +
310B ALA* 3.4 11.3 - - - +
340B THR* 4.2 12.2 - - + +
365B ASN* 3.9 0.4 - - - -
367B PHE* 3.3 1.4 - - - -
1M NAG 3.3 24.1 + - - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il